Do patterns of phylogenesis show evolution?

[Difflugia]

Question for debate: Are the patterns seen in molecular phylogenies sufficient to show that biological evolution occurred?

For reference and easier Googling, the science of generating evolutionary trees is known as cladistics or phylogenetic systematics. Using DNA sequence data to generate the trees is molecular phylogeny.

The standard of evidence I'll be discussing is reasonable doubt. Even that's pretty broad, but if your argument hinges on "possible," you should be able to at least quantify that.

I've generated phylogenies using online tools previously and discussed them in this post. I tried to start a tutorial in this thread. If someone wants to discuss how to actually use the tools and data, feel free to ask questions in the tutorial thread and I'll pick it back up.

This debate question is a response to this comment.

[Jose Fly]

The theory of evolution and the so called evidence supporting it, is dubious on their own merits.

But you can't know that since you've never looked at the evidence nor do you know much of anything at all about the science. All you have to go on is what a handful of creationists have told you....and nothing else. And since you know nothing about the science, you can't possibly know if what the creationists tell you is accurate.

You keep setting yourself up for embarrassment by trying to debate a scientific subject you know nothing about. Might want to rethink that.

[Clownboat]

Jesus would be proud of unbelievers in him, pushing a false theory which undermines his word?

No silly. Jesus would be proud of the patience we have to continue attempting to educate how actual evolution works. You simply deny that an all powerful God can be all powerful for some reason, but it is still possible that a God created life and evolution is how we got to the life we see both in the fossil record and now on earth.

I find your denial unjustified and await valid reasoning to explain why it is a justifiable belief (if there exists such a reason).

In a nut shell, the main idea as to why we don't see these macro level changes in nature is because "not enough time has elapsed. Give it a few hundred million years, and you'll see".

We see the changes in the fossil record though.
Let's say for a minute that your drive to work takes you 30 minutes. It would not be valid for me to reject your drive to work just because you cannot do it in 5 minutes. We are basically showing you the route, putting it in more easily understood terms and you are rejecting it because it takes too long.

Since we know that changes in populations do take place, you must come up with a valid mechanism that stops the changes from happening at some point. If you cannot, it is only logical that continued changes will continue to cause the said population to change.

As you have learned, a population in Spain for one animal may become a seemingly different animal in Italy due to different changes in the population taking place in Italy. (Relating back to language in hopes to make it easier to understand).

You see, if Mother Nature is the "God" of evolution, then "time" is the holy spirit of Mother Nature.

Please show that this Mother Nature you mention is a real thing or admit you are interjecting make believe in order to try to level the playing field.

You can't have evolution without the power of "time".

Correct. Just like you cannot walk a mile without taking many small steps, therefore your complaint is found to be odd. What's logical for traveling a mile (many small steps) is logical for changes in populations (changes over time/steps) adding up. Unless of course you can identify a mechanism that at some point stops the small changes from occurring. If there is no such mechanism, Latin will become both Spanish and Italian after enough steps.

Have animals copulate, sprinkle a a little hundred million years in there, and viola.

You have forgotten all about what you learned about how languages evolved. Why are you leaving out the small changes within differing populations, something we observe happening currently? This is crucial and will help for it to not sound like magic to you.

No one living today will ever see it, because we are too late..we missed it by a few hundred million years.

Let's test to see if your criticism is valid and consistent shall we.
Have you ever witnessed a liquifying dead body reanimate to life, or a God creating life?

Your criticism is invalid and not consistent and it denies what we see in the fossil record.

The people living a hundred million years from now will be told the same thing.

"Sorry, buddy. Party's over. You missed it".

Invalid and inconsistent reasoning that must be rejected.

If you guys can't see the scam, the lie, the fraud in that, then I don't know what to tell you.

I see this as nothing but denial without any substance.
Are you claiming to have a better mechanism to explain what we see now and in the fossil record? Does your explanation agree with the fossil record, biogeography and DNA? Can it make predictions about where we will find undiscovered fossils and what they should look like?

"Tiktaalik," a transitional fossil between fish and land animals, which was found in the Ellesmere Island region of Canada, precisely where scientists predicted it would be based on its evolutionary timeline and geological conditions; this discovery strongly validated the predictions made by evolutionary theory about where such a fossil should be located.

Who said Noah was born in a manger?

Perhaps someone that would ask to see a whale give birth to a mouse?

Oh, it is easily understood...it just ain't happen.

Once again you have nothing but denial. You are unable to show that what you believe is logical. If you can provide something more than denial, I would love to see it.

I say the same thing when it comes to getting you guys to accept Christ.

The difference between you and I is that I have drank the said water and I understand it. You have not drank, nor do you have a good understanding of evolution. So you can say the same thing, but it will be received as being silly.

Can you address this, it is very important?:
Since we know that changes in populations do take place, you must come up with a valid mechanism that stops the changes from happening at some point. What would prevent Latin from becoming Spanish and Italian in evolutionary terms?

[Clownboat]

1) What if there was a God that created life and then the mechanism of evolution?

Bible believers like me know that speculation involves bad assumptions and perverse reasoning.

This failed to address what was asked of you and is just you telling me what you believe. You know, like someone on a street corner shouting their beliefs at people.

That would mean that evolution is in fact intelligent and not accidental. Why are you willing to rule out the idea that gods did this?

There is one Creator God who created all living beings after their own kinds.

Again, you shout in my face (metaphorically) and failed to address that if a God created the process of evolution, it would be intelligent and not accidental like your previous claim.

2) What is your reason for assuming that all powerful beings could not create life and then a process where it changes?

I don't really have time to discuss speculations that can never be proven and that border on myths and wild imaginations.

This is nothing but an excuse for not addressing an assumption (you assume that an all powerful God could not create life and then use the process of evolution) you make without any evidence nor reason.

3) In regards to the nylon eating bacteria (nylon is man made and doesn't exist in nature). Do you believe that your preferred God created this bacteria, or that the earth brought it forth?

God brought forth all original life and science has adequately demonstrated that no life is ever formed by non-life.

Again, this is just a claim. Can you not get off your soap box, just for a minute?

4) Did all 400,000 species of beetle evolve from a single male and female that was on a boat just some thousands of years ago, or were the 399,999 created by your preferred way after the fact?

God created beetles with the ability to adapt and change, but not to evolve into Princeton professors.

Doesn't answer the question. Nothing but failure from you I note in this response.
Readers, make of it what you will and then ask yourself if their denial and empty claims are justified.

The Islamic gods are not real gods at all.[/b]

That can't be true because the Islamic Gods beat up your Gods.
I can make silly claims to that are meaningless in debate too!

[Difflugia]

The molecular data don't support a common designer that reuses common elements. In situations where organisms share genes with identical functions, those genes still show divergence that exactly matches that of other genes. Would your idea of a common designer design in a way that exactly matches what we expect from evolution? If not, what clues should we expect to find in the genomic data?

Let's put this one to bed, Diff.

Your theory presupposes life, PERIOD.

The life that your theory presupposes, ain't originating without a Cosmic Creator (CC).

So, you're now giving up on the argument from common design? If you're not, then you haven't addressed my question at all, let alone "put this one to bed."

The argument from common design is that any apparent phylogenetic pattern is because Jesus reused similar structural elements to perform similar functions. This is belied by genes with highly conserved functionality, though. Proteins with identical functions still show the same pattern of structural differences. Why is that? Why would Jesus choose to design using proteins that differ in structure even when they perform identical functions?

[Clownboat]

It leads to falsehoods, misled youths, wasted tax payers money, and most importantly, a distortion of God's word, and actions.

So, you are correct; I don't like where it leads.

If you are able to set your pride aside for just a moment, because your understanding about evolution is lacking, consider that your claims above just might not be correct.

Making claims over and over, without providing evidence and complaining about the current best available explanation that is open to being shown incorrect is all you are doing (plus straight out denial) and this doesn't support your claims.

Show a Rabbit in the Cambrian layer and evolution is now false, or provide one animal giving birth to another and evolutions is now false, or provide a mechanism that prevents mutations from accumulating over time within a population and evolution is now false, or provide examples of species being created supernaturally, or provide a better explanation and it must be considered.

There are many valid things that can be done to at least suggest that the ToE is not the best explanation. Currently what we are hearing is not valid though, just faith based claims without evidence and straight out denial.

[SiNcE_1985]

^^

[SiNcE_1985]

So, you're now giving up on the argument from common design?

Somebody tell this guy that common designer and cosmic creator are the same thing.

If you're not, then you haven't addressed my question at all, let alone "put this one to bed."

The argument from common design is that any apparent phylogenetic pattern is because Jesus reused similar structural elements to perform similar functions. This is belied by genes with highly conserved functionality, though. Proteins with identical functions still show the same pattern of structural differences. Why is that? Why would Jesus choose to design using proteins that differ in structure even when they perform identical functions?

I've always responded to this in my last response to you.

We are well past repeating the same stuff over again.

I'm gonna keep my responses short unless something new is presented.

Like I said, time to put this one to bed.

[The Barbarian]

Show me anyone who has seen a mountain range erode down from high peaks to low hills.

First of all, I am unfamiliar with particular claims as it relates to this, and if something isn't adding up with this, then I'll reject it as well...the same way I do with evolutionary claims.

Doesn't matter. Reality shows it happens and we can watch it happening now. We just don't live long enough to watch the whole process. No point in denying it, though.

Second, it isn't just the fact that I find the evidence presented for evolution to be lacking and unpersuasive, but I also have evidence AGAINST it.

Since we see it going on constantly in populations around us, your disbelief isn't really very convincing. I suspect you've confused evolution (which is an observed phenomenon) with common descent, which is a consequence of evolution.

This is the last defense of the YE creationist, when he realizes all the evidence is arrayed against his modern revision of scripture. "No one ever lived long enough to see ... (whatever millions of years evolution)" [/quote]

So, if someone said that nature has a way of giving your family X amount of money every so often.

This concept is called "Moneylution".

You ask for the money, and you are told "It has already given your ancestors the money, centuries ago".

You ask, well, when will my current, living family get the money?

That's where your analogy falls apart. Because we see changes in allele frequency constantly in nature, your analogy would have each of us being given money on a regular basis.

But to address your question more deeply, tell me what feature of birds is not also found in other dinosaurs. We can then look at the issue rationally, determining what evidence there is for evolution of that trait. What do you have?

So, let me get this straight, you mean to tell me that since..

I'd like you to show me even one feature of birds not found in dinosaurs. If you can't, by default, birds are dinosaurs.

1. A Boeing 747 airplane has 18 wheels, a steering wheel, and an engine.

And..

2. A typical semi truck with trailer also has 18 wheels, a steering wheel, and an engine.

3. Conclusion: That since they both have similar features, that therefore, one clearly evolved from the other!!!

I can show you lots of features of airplanes not found in trucks. But you seem to realize that there isn't one feature of birds not found in dinosaurs. If you felt that you had to misrepresent my argument to make a point, isn't that a pretty good clue about your argument?

I was a fool for ever doubting evolution!!

I think you're just so deeply indoctrinated in false doctrines that you are unable to free yourself.

Wolves and dogs are in the same family. Canidae. Just like humans, chimpanzees, gorillas, and bonobos are all in the same family Hominidae. So by your revision of "microevolution", the common descent of humans and other apes is "microevolution." You sure you want to do that? I would think you'd want to stay with the actual definition of the word.

Rock and hard place.

I would take humans out of the equation...

It's normal for many YE creationists to simply deny facts the way you have here. But the facts remain. Your standard for "kinds" puts humans and chimpanzees in the same "kind." No way to dodge it.

it contradicts scripture...

No, it contradicts your revision of scripture, but you've been doing that for a while now. Why not just set your pride aside, and let it be God's way?
As you just realized, your man-made belief in "kinds" puts humans and chimpanzees and gorillas in the same "kind."

That is exactly what I'm not saying.

That's exactly what you're saying. Unless you want to redefine "kind" one more time. What will it be?

God says it is. I believe Him. You should, too.

You deny abiogenesis, which God tells us is the way He created living things in the beginning. You deny evolution which is observed going on in all living populations.
Why not just accept it His way?

Still conflating a concept that is by definition, supposed to happen without God (abiogenesis), with a concept that takes occurs with God (creation).

You've just tried to add religious context to science. Science doesn't say how the universe started. It just points out that the earth brought forth life. That's God's opinion, too. Why are you surprised that Christians would take His word over yours?

Well, since you brought that up, let's ask one of the guys who invented the concept of "intelligent design":
"it is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science - that the cosmos is a seamless unity which can be comprehended ultimately in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called "special creationist school". According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world - that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies."
IDer, and Discovery Institute Fellow Michael Denton Nature's Destiny (page xvii-xviii). [/quote]

I won't respond to this until I have a lawyer present.

Odd you should say that. ID was more or less the invention of Philip Johnson, a lawyer and founder of the Discovery Institute, along with Mike Denton. How about that? The point is, IDers who are scientists like Denton and Behe are evolutionists. They just think the "designer" (Denton's idea) or God (Behe's idea) started it all.

But the "days" of creation can't be normal days, because you can't have mornings and evenings without a sun to have them. Once again, you've added things to scripture to make it more acceptable to you.

No, God was already distinguishing night from day, as early as Gen 1:3-4,

Which is how we know that the "yom" (God didn't say "days") are not literal 24 hour days. So, regardless of how/what you perceive a day to be, God was doing his own thing, not caring about what his creation (you) would think.

Perhaps it would benefit you to actually read Genesis. If you obsess on these things, you miss the entire message of Genesis. Not that you'll go to hell for being a YE creationist. But if you'd be willing to accept all of His word as it is, you'd have a better relationship with Him. Instead, you're trying to fit a dumb, manmade theory into the Bible, is what have you lost...and it is insulting to God.

Sounds familiar.

YE creationism, summed up.

[The Barbarian]

You have your reasons why you reject Christianity, and I have my reasons why I reject evolution.

Why not accept both truths and just take it God's way?

[SiNcE_1985]

No silly. Jesus would be proud of the patience we have to continue attempting to educate how actual evolution works.

No, you just don't understand Christianity, if that's what you think about Jesus.

You simply deny that an all powerful God can be all powerful for some reason, but it is still possible that a God created life and evolution is how we got to the life we see both in the fossil record and now on earth.

?

I find your denial unjustified and await valid reasoning to explain why it is a justifiable belief (if there exists such a reason).

I poured everything I can into these discussions.

What you saw, is what you got.

We see the changes in the fossil record though.

We don't, though.

That is what your presupposition tells you, not what the fossil tells you.

Let's say for a minute that your drive to work takes you 30 minutes.

It would not be valid for me to reject your drive to work just because you cannot do it in 5 minutes.

We are basically showing you the route, putting it in more easily understood terms and you are rejecting it because it takes too long.

I'm not rejecting it because it takes to long, I reject it because I have no reason to conclude that it can ever begin in the first place, on atheism.

Since we know that changes in populations do take place, you must come up with a valid mechanism that stops the changes from happening at some point.

The valid mechanism is abiogenesis, which ensures that it won't happen at all.

If you cannot, it is only logical that continued changes will continue to cause the said population to change.

It is only logical that, until you have a viable theory as to how life originated from nonlife, you cannot have life evolving into or from anything.

As you have learned, a population in Spain for one animal may become a seemingly different animal in Italy due to different changes in the population taking place in Italy. (Relating back to language in hopes to make it easier to understand).

Um, no one is denying that. That ain't got nothing to do with a reptile evolving into a bird.

Please show that this Mother Nature you mention is a real thing or admit you are interjecting make believe in order to try to level the playing field.

Ummm.

nature personified as a woman considered as the source and guiding force of creation

https://www.merriam-webster.com/diction ... r%20Nature

And I'm supposed to be the ignorant one here?

Smh.

Correct. Just like you cannot walk a mile without taking many small steps, therefore your complaint is found to be odd.

What's logical for traveling a mile (many small steps) is logical for changes in populations (changes over time/steps) adding up. Unless of course you can identify a mechanism that at some point stops the small changes from occurring. If there is no such mechanism, Latin will become both Spanish and Italian after enough steps.

The only evidence we have for those small changes, remains at the micro level.

That is the extent of our observed knowledge.

To assume that there isn't a limit to the changes, is to leave science (observable, testable knowledge) and to arrive on fantasy island...as you are relying on the unseen, the untested, the indemonstrable.

You have forgotten all about what you learned about how languages evolved. Why are you leaving out the small changes within differing populations, something we observe happening currently? This is crucial and will help for it to not sound like magic to you.

As I said in a prior post, your language analogy is one of micro.

Get me Latin to Korean, Vietnamese, Chinese, or Arabic.

Then, you'll have something.

Let's test to see if your criticism is valid and consistent shall we.
Have you ever witnessed a liquifying dead body reanimate to life, or a God creating life?

Already addressed this.

Your criticism is invalid and not consistent and it denies what we see in the fossil record.

And this.

Invalid and inconsistent reasoning that must be rejected.

Opinions.

I see this as nothing but denial without any substance.
Are you claiming to have a better mechanism to explain what we see now and in the fossil record? Does your explanation agree with the fossil record, biogeography and DNA? Can it make predictions about where we will find undiscovered fossils and what they should look like?

What fossil record?

When you see a fossil..

Correct interpretation: Here are the remains of a once living organism.

Fantasyland Interpretation: Here are the remains of a once living organism, and it is the evolutionary predecessor of X living organism.

Interpretation #1 is the only thing you can conclude when you find a fossil.

Interpretation #2 is what you conclude when you have a presupposition, and this presupposition is the guiding force behind how you are going to interpret the observation.

"Tiktaalik," a transitional fossil between fish and land animals, which was found in the Ellesmere Island region of Canada, precisely where scientists predicted it would be based on its evolutionary timeline and geological conditions; this discovery strongly validated the predictions made by evolutionary theory about where such a fossil should be located.

Welcome to fantasy island. None of that stuff happened.

Where are the rest of the transitional fossils within that chain?

Tell me.

Perhaps someone that would ask to see a whale give birth to a mouse?

Wait a minute...

On one hand, just above, you just asked the question of "What is the mechanism that will allow the changes in populations to stop, over time".

Now, on the other hand, your above quote is insinuating that there in fact a limitation to the changes in populations, as you are light-heartedly mocking the idea of a whale giving birth to a mouse (instant or gradual evolution).

Tsk, tsk.

Once again you have nothing but denial. You are unable to show that what you believe is logical. If you can provide something more than denial, I would love to see it.

Abiogenesis, and I explained why.

Yes, the theory that no one wants to talk about.

You mention abiogenesis, and evolutionists shudder.

The difference between you and I is that I have drank the said water and I understand it. You have not drank, nor do you have a good understanding of evolution. So you can say the same thing, but it will be received as being silly.

No, I don't think you understand Christianity... otherwise, you'd believe it.

Sounds crazy, doesn't it?

Well, that's how it sounds when you accuse me of not understanding evolution.

I understand evolution just as much as you understand Christianity.

Can you address this, it is very important?:
Since we know that changes in populations do take place, you must come up with a valid mechanism that stops the changes from happening at some point. What would prevent Latin from becoming Spanish and Italian in evolutionary terms?

Already addressed this.